grinch | global report investigating novel coronavirus haplotypes

B.1.351 report 2021-01-12



Description

South African lineage defined by new variant 501Y.V2 - A more detailed description of the lineage is here and a preprint describing the variant is here

Data source and processing

This report is recent as of 2021-01-12 20:01 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.6, pangoLEARN version 2020-12-17-2.

Pangolin assigns B.1.351 to any sequences with more than 5 of the 9 defining B.1.351 SNPs, defined in the preprint here.

Table 1 | Summary of sequence data

Lineage Country count Country Sequence count Earliest sequence Travel history
B.1.351 12 South_Africa 349, UK 35, Botswana 6, Australia 5, Germany 3, Ireland 3, Switzerland 2, France 2, Finland 1, Netherlands 1, South_Korea 1, Sweden 1 409 2020-10-08

Lineage B.1.351

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.351 | Lineage B.1.351

Statistic Information
Count 409
Likely origin South Africa
SNPs aa:E:P71L
aa:N:T205I
aa:orf1a:K1655N
aa:S:D80A
aa:S:D215G
aa:S:K417N
aa:S:A701V
aa:S:N501Y
aa:S:E484K

Figure 1 | Cumulative sequence count over time B.1.351

2021-01-12T22:02:09.633649 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 2 | Date of earliest B.1.351 detected

2021-01-12T22:02:08.779497 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 3 | Map of B.1.351 sequence counts

2021-01-12T22:02:09.017518 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 4 | Sequence count per country B.1.351

2021-01-12T22:02:09.200628 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country

2021-01-12T22:02:09.780012 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 6 | B.1.351 count per country

2021-01-12T22:02:10.082471 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 7 | Rolling average B.1.351 frequency per country

2021-01-12T22:02:09.938341 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 8 | Map of B.1.351 local transmission

2021-01-12T22:02:08.131979 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 9 | Air traffic from South Africa by destination

The number of ticketed origin-to-destination journeys from South African airports to countries outside South Africa during October 2020.

Colours indicate numbers of published genomes of B.1.351 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.351 sequences on GISAID. White bars indicate countries with no reports of B.1.351.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >300 passengers.

Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased. Also, this data will not reflect volume of traffic over land or other modes of transport.

Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer

2021-01-12T22:02:08.476255 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Table 2 | Reported B.1.351 imports.

Country count: 15

Country Earliest report Date local transmission Local transmission Method of surveillance Source
South Africa 2020-10-08 2020-10-08 1 community_sequencing https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1
United Kingdom 2020-12-12 2020-12-20 1 community_sequencing https://travelhealthpro.org.uk/news/561/covid-19-variant-south-africa-two-cases-reported-in-the-united-kingdom
Switzerland 2020-12-14 0 https://www.swissinfo.ch/eng/south-african-covid-variant-reported-in-southern-switzerland/46257338
Finland 2020-12-19 0 travellers https://news.sky.com/story/covid-19-finland-reports-cases-of-new-variants-first-identified-in-uk-and-south-africa-12173983
Zambia 2020-12-30 2020-12-30 1 https://twitter.com/danieljbridges/status/1344227535870164992
Botswana 2020-12-17 2021-01-04 1 community_sequencing https://www.sabcnews.com/sabcnews/botswana-government-adjusts-national-lockdown-regulations/
France 2020-12-31 0 travellers https://www.france24.com/en/france/20201231-france-detects-first-case-of-south-african-strain-of-covid-19
Japan 2020-12-19 0 travellers https://www.japantimes.co.jp/news/2020/12/29/national/japan-south-africa-variant/
Australia 2020-12-22 0 travellers https://news.sky.com/story/australia-reports-its-first-case-of-south-africa-coronavirus-variant-12174611
Sweden 2021-01-03 0 travellers http://outbreaknewstoday.com/sweden-reports-1st-south-african-covid-19-virus-variant-49394/
Austria 2021-01-04 0 https://www.sn.at/panorama/wissen/live-corona-mutationen-sind-in-oesterreich-angekommen-97891537
Norway 2020-12-31 0 travellers https://www.vg.no/nyheter/innenriks/i/rgzer8/mer-smittsom-virusmutasjon-fra-soer-afrika-paavist-i-norge
China 2020-12-08 0 travellers https://news.cgtn.com/news/2021-01-06/Guangdong-detects-first-COVID-19-case-of-variant-found-in-S-Africa-WPW5sbHcju/index.html
Ireland 2021-01-08 0 travellers https://www.reuters.com/article/health-coronavirus-ireland/south-african-covid-19-variant-present-in-ireland-health-chief-idINS8N2II031
Canada 2021-01-08 0 travellers https://www.sylvanlakenews.com/news/south-african-covid-19-found-in-alberta-as-provinces-tighten-restrictions/
Germany 2020-12-21 0 travellers https://www.dw.com/en/south-african-covid-variant-found-in-germany/a-56205752